Self-test failure (IR -> REF)

Using the Pioreactor
1

Hi,
First, I would like to say that this is a great initiative and I wish you every success in making bioreactors more accessible to scientific community.

I have recently bought two Pioreactors (v1.1) and, after following the instructions, have both successfully assembled and connected to Wi-Fi. I tried to run a self-test after that and ran into a problem with the apparent absence of a linear response between the IR LED and the photodiode in Channel 2 (90°). Both pioreactors appear to have the same problem. Would you have any suggestions/recommendations?

Event log

timestamp_localtime experiment pioreactor_unit timestamp message source level task
2024-06-08 18:24:11 Demo experiment pio1 2024-06-08T17:24:11.082246Z Starting self-test. Running 10 tests. app INFO self_test
2024-06-08 18:24:11 Demo experiment pio1 2024-06-08T17:24:11.097642Z test_pioreactor_HAT_present: :white_check_mark: app DEBUG self_test
2024-06-08 18:24:11 Demo experiment pio1 2024-06-08T17:24:11.168879Z test_detect_heating_pcb: :white_check_mark: app DEBUG self_test
2024-06-08 18:24:11 Demo experiment pio1 2024-06-08T17:24:11.203648Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-08 18:24:11 Demo experiment pio1 2024-06-08T17:24:11.209276Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-08 18:24:11 Demo experiment pio1 2024-06-08T17:24:11.688698Z Varying heating. app DEBUG self_test
2024-06-08 18:24:24 Demo experiment pio1 2024-06-08T17:24:24.848576Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-08 18:24:26 Demo experiment pio1 2024-06-08T17:24:26.769977Z Correlation between temp sensor and heating: 0.97 app DEBUG self_test
2024-06-08 18:24:32 Demo experiment pio1 2024-06-08T17:24:32.784771Z test_positive_correlation_between_temperature_and_heating: :white_check_mark: app DEBUG self_test
2024-06-08 18:24:32 Demo experiment pio1 2024-06-08T17:24:32.790786Z test_aux_power_is_not_too_high: :white_check_mark: app DEBUG self_test
2024-06-08 18:24:59 Demo experiment pio1 2024-06-08T17:24:59.059281Z Corr(A, 1) = 1.0 app DEBUG self_test
2024-06-08 18:24:59 Demo experiment pio1 2024-06-08T17:24:59.062708Z [(32, 0.09645419933229045), (35, 0.09863152973425277), (53, 0.11572266720108727), (44, 0.10694855621697068), (38, 0.1010654856629908), (47, 0.10974609466771185), (50, 0.11248344743076988), (41, 0.10372681994955281), (56, 0.11741680768698169), (59, 0.11951920442257775), (62, 0.12179782007547761), (65, 0.12407002190842785)] app DEBUG self_test
2024-06-08 18:24:59 Demo experiment pio1 2024-06-08T17:24:59.065207Z Corr(A, 2) = 0.19 app DEBUG self_test
2024-06-08 18:24:59 Demo experiment pio1 2024-06-08T17:24:59.067873Z [(32, 0.06084120269870052), (35, 0.060787022342132215), (53, 0.06085038936309487), (44, 0.060832446706653866), (38, 0.06082527310980005), (47, 0.06080620350511639), (50, 0.060868109958803464), (41, 0.06086673978829251), (56, 0.060865090831338724), (59, 0.06088069658611994), (62, 0.06082999921213661), (65, 0.060801631753397346)] app DEBUG self_test
2024-06-08 18:25:02 Demo experiment pio1 2024-06-08T17:25:02.137026Z Correlations between LEDs and PD:
{(‘A’, ‘1’): 1.0, (‘A’, ‘2’): 0.19}		 app DEBUG self_test
2024-06-08 18:25:02 Demo experiment pio1 2024-06-08T17:25:02.155889Z missing A ⇝ 2
Traceback (most recent call last):
File /usr/local/lib/python3.11/dist-packages/pioreactor/actions/self_test.py, line 441, in _run
test(client, logger, unit, testing_experiment)
File /usr/local/lib/python3.11/dist-packages/pioreactor/actions/self_test.py, line 232, in test_all_positive_correlations_between_pds_and_leds
assert results[(ir_led_channel, ir_pd_channel)] > 0.90, fmissing {ir_led_channel} ⇝ {ir_pd_channel}
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: missing A ⇝ 2		 app DEBUG self_test
2024-06-08 18:25:02 Demo experiment pio1 2024-06-08T17:25:02.161603Z test all positive correlations between pds and leds: missing A ⇝ 2 app WARNING self_test
2024-06-08 18:25:02 Demo experiment pio1 2024-06-08T17:25:02.164187Z test_all_positive_correlations_between_pds_and_leds: :x: app DEBUG self_test
2024-06-08 18:25:02 Demo experiment pio1 2024-06-08T17:25:02.170905Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-08 18:25:02 Demo experiment pio1 2024-06-08T17:25:02.175669Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-08 18:25:03 Demo experiment pio1 2024-06-08T17:25:03.172224Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-08 18:25:03 Demo experiment pio1 2024-06-08T17:25:03.177750Z test_ambient_light_interference: :white_check_mark: app DEBUG self_test
2024-06-08 18:25:03 Demo experiment pio1 2024-06-08T17:25:03.184253Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-08 18:25:03 Demo experiment pio1 2024-06-08T17:25:03.187774Z ADC ready to read from PD channels 1, with gain 1. app DEBUG adc_reader
2024-06-08 18:25:04 Demo experiment pio1 2024-06-08T17:25:04.091515Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-08 18:25:04 Demo experiment pio1 2024-06-08T17:25:04.095890Z ADC offsets: {‘1’: 1191.189088519811}, and in voltage: {‘1’: 0.05999578742544835} app DEBUG adc_reader
2024-06-08 18:25:09 Demo experiment pio1 2024-06-08T17:25:09.603175Z test_REF_is_lower_than_0_dot_256_volts: :white_check_mark: app DEBUG self_test
2024-06-08 18:25:10 Demo experiment pio1 2024-06-08T17:25:10.204880Z Not using any IR LED reference. app DEBUG ir_led_ref
2024-06-08 18:25:10 Demo experiment pio1 2024-06-08T17:25:10.219931Z Not using any calibration. app DEBUG calibration_transformer
2024-06-08 18:25:10 Demo experiment pio1 2024-06-08T17:25:10.525052Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-08 18:25:10 Demo experiment pio1 2024-06-08T17:25:10.529743Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-08 18:25:11 Demo experiment pio1 2024-06-08T17:25:11.571679Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-08 18:25:12 Demo experiment pio1 2024-06-08T17:25:12.478187Z ADC offsets: {‘1’: 1189.9392335983885, ‘2’: 1205.9044983204165}, and in voltage: {‘1’: 0.05993283685706168, ‘2’: 0.060736948175478846} app DEBUG adc_reader
2024-06-08 18:26:20 Demo experiment pio1 2024-06-08T17:26:20.928878Z test_REF_is_in_correct_position: :white_check_mark: app DEBUG self_test
2024-06-08 18:26:20 Demo experiment pio1 2024-06-08T17:26:20.932573Z Not using any IR LED reference. app DEBUG ir_led_ref
2024-06-08 18:26:20 Demo experiment pio1 2024-06-08T17:26:20.935085Z Not using any calibration. app DEBUG calibration_transformer
2024-06-08 18:26:21 Demo experiment pio1 2024-06-08T17:26:21.340671Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-08 18:26:21 Demo experiment pio1 2024-06-08T17:26:21.344716Z ADC ready to read from PD channels 2, with gain 1. app DEBUG adc_reader
2024-06-08 18:26:22 Demo experiment pio1 2024-06-08T17:26:22.383604Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-08 18:26:23 Demo experiment pio1 2024-06-08T17:26:23.288232Z ADC offsets: {‘2’: 1207.17262311265}, and in voltage: {‘2’: 0.060800818929666434} app DEBUG adc_reader
2024-06-08 18:26:38 Demo experiment pio1 2024-06-08T17:26:38.106872Z test_PD_is_near_0_volts_for_blank: :white_check_mark: app DEBUG self_test
2024-06-08 18:27:09 Demo experiment pio1 2024-06-08T17:27:09.600147Z Correlation between stirring RPM and duty cycle: 0.99 app DEBUG self_test
2024-06-08 18:27:09 Demo experiment pio1 2024-06-08T17:27:09.603090Z dcs=[36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], measured_rpms=[1037.196297310795, 1000.2475422143299, 999.9792711779794, 891.189376940555, 811.8439227102607, 738.0839619589477, 674.8476718497708, 606.1162458993286] app DEBUG self_test
2024-06-08 18:27:12 Demo experiment pio1 2024-06-08T17:27:12.730862Z test_positive_correlation_between_rpm_and_stirring: :white_check_mark: app DEBUG self_test
2024-06-08 18:27:12 Demo experiment pio1 2024-06-08T17:27:12.734923Z 1 failed test :x: app INFO self_test

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2

Hi @TimSkvortsov, thanks for the kind words!

This has been reported by some other users, and we are working on making this test more robust. Try the following:

  1. Add a slight volume of culture, or milk, or tea, or anything that is turbid (cloudy) to your vial. The goal is to add a little more light scatter to the culture.
  2. Try the self-test again (if other tests fail now, that’s okay and can be ignored)
3

Hi @CamDavidsonPilon, thanks for your suggestion, it fixed the problem with photodiodes.

I have another problem with one of the bioreactors now unfortunately – the magnetic stirrer seems to stop randomly during the self-test.

2024-06-10 14:47:35 Demo experiment pio1-worker1 2024-06-10T13:47:35.777319Z Starting self-test. Running 10 tests. app INFO self_test
2024-06-10 14:47:35 Demo experiment pio1-worker1 2024-06-10T13:47:35.786376Z test_pioreactor_HAT_present: :white_check_mark: app DEBUG self_test
2024-06-10 14:47:35 Demo experiment pio1-worker1 2024-06-10T13:47:35.861074Z test_detect_heating_pcb: :white_check_mark: app DEBUG self_test
2024-06-10 14:47:35 Demo experiment pio1-worker1 2024-06-10T13:47:35.912888Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:47:35 Demo experiment pio1-worker1 2024-06-10T13:47:35.947813Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-10 14:47:36 Demo experiment pio1-worker1 2024-06-10T13:47:36.364185Z Varying heating. app DEBUG self_test
2024-06-10 14:47:48 Demo experiment pio1-worker1 2024-06-10T13:47:48.880309Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:47:51 Demo experiment pio1-worker1 2024-06-10T13:47:51.149979Z Correlation between temp sensor and heating: 0.98 app DEBUG self_test
2024-06-10 14:47:56 Demo experiment pio1-worker1 2024-06-10T13:47:56.386620Z test_positive_correlation_between_temperature_and_heating: :white_check_mark: app DEBUG self_test
2024-06-10 14:47:56 Demo experiment pio1-worker1 2024-06-10T13:47:56.391835Z test_aux_power_is_not_too_high: :white_check_mark: app DEBUG self_test
2024-06-10 14:48:21 Demo experiment pio1-worker1 2024-06-10T13:48:21.123161Z Corr(A, 1) = 1.0 app DEBUG self_test
2024-06-10 14:48:21 Demo experiment pio1-worker1 2024-06-10T13:48:21.125721Z [(32, 0.09827861250919949), (35, 0.10058657476195744), (53, 0.11663276682271405), (44, 0.10807902007202656), (38, 0.10259237032963303), (47, 0.1107397506570529), (50, 0.11324634013075248), (41, 0.10501456769659434), (56, 0.11785385423486877), (59, 0.11975806111292342), (62, 0.1219027642740242), (65, 0.124067474579029)] app DEBUG self_test
2024-06-10 14:48:21 Demo experiment pio1-worker1 2024-06-10T13:48:21.128146Z Corr(A, 2) = 0.99 app DEBUG self_test
2024-06-10 14:48:21 Demo experiment pio1-worker1 2024-06-10T13:48:21.130678Z [(32, 0.0650443583001459), (35, 0.06508283175166249), (53, 0.06532350630570133), (44, 0.06517065063390019), (38, 0.06513288813812566), (47, 0.06526349078929809), (50, 0.06528957855681405), (41, 0.06516690760752165), (56, 0.06537353862511312), (59, 0.06544855227219769), (62, 0.06548641194047634), (65, 0.06551454218697256)] app DEBUG self_test
2024-06-10 14:48:24 Demo experiment pio1-worker1 2024-06-10T13:48:24.323431Z Correlations between LEDs and PD:
{(‘A’, ‘1’): 1.0, (‘A’, ‘2’): 0.99}		 app DEBUG self_test
2024-06-10 14:48:24 Demo experiment pio1-worker1 2024-06-10T13:48:24.326632Z test_all_positive_correlations_between_pds_and_leds: :white_check_mark: app DEBUG self_test
2024-06-10 14:48:24 Demo experiment pio1-worker1 2024-06-10T13:48:24.330898Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:48:24 Demo experiment pio1-worker1 2024-06-10T13:48:24.334450Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-10 14:48:25 Demo experiment pio1-worker1 2024-06-10T13:48:25.338187Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:48:25 Demo experiment pio1-worker1 2024-06-10T13:48:25.342475Z test_ambient_light_interference: :white_check_mark: app DEBUG self_test
2024-06-10 14:48:25 Demo experiment pio1-worker1 2024-06-10T13:48:25.346680Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:48:25 Demo experiment pio1-worker1 2024-06-10T13:48:25.349449Z ADC ready to read from PD channels 1, with gain 1. app DEBUG adc_reader
2024-06-10 14:48:26 Demo experiment pio1-worker1 2024-06-10T13:48:26.252815Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:48:26 Demo experiment pio1-worker1 2024-06-10T13:48:26.256261Z ADC offsets: {‘1’: 1271.6542551979765}, and in voltage: {‘1’: 0.06404852017938525} app DEBUG adc_reader
2024-06-10 14:48:31 Demo experiment pio1-worker1 2024-06-10T13:48:31.762118Z test_REF_is_lower_than_0_dot_256_volts: :white_check_mark: app DEBUG self_test
2024-06-10 14:48:32 Demo experiment pio1-worker1 2024-06-10T13:48:32.394744Z Not using any IR LED reference. app DEBUG ir_led_ref
2024-06-10 14:48:32 Demo experiment pio1-worker1 2024-06-10T13:48:32.419212Z Not using any calibration. app DEBUG calibration_transformer
2024-06-10 14:48:32 Demo experiment pio1-worker1 2024-06-10T13:48:32.750650Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:48:32 Demo experiment pio1-worker1 2024-06-10T13:48:32.754195Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-10 14:48:33 Demo experiment pio1-worker1 2024-06-10T13:48:33.790786Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:48:34 Demo experiment pio1-worker1 2024-06-10T13:48:34.696519Z ADC offsets: {‘1’: 1270.6061365996763, ‘2’: 1277.8046966548184}, and in voltage: {‘1’: 0.06399573032324377, ‘2’: 0.06435829516118591} app DEBUG adc_reader
2024-06-10 14:49:51 Demo experiment pio1-worker1 2024-06-10T13:49:51.527375Z test_REF_is_in_correct_position: :white_check_mark: app DEBUG self_test
2024-06-10 14:49:51 Demo experiment pio1-worker1 2024-06-10T13:49:51.530915Z Not using any IR LED reference. app DEBUG ir_led_ref
2024-06-10 14:49:51 Demo experiment pio1-worker1 2024-06-10T13:49:51.533088Z Not using any calibration. app DEBUG calibration_transformer
2024-06-10 14:49:51 Demo experiment pio1-worker1 2024-06-10T13:49:51.965982Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:49:51 Demo experiment pio1-worker1 2024-06-10T13:49:51.969085Z ADC ready to read from PD channels 2, with gain 1. app DEBUG adc_reader
2024-06-10 14:49:53 Demo experiment pio1-worker1 2024-06-10T13:49:53.008096Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:49:53 Demo experiment pio1-worker1 2024-06-10T13:49:53.911972Z ADC offsets: {‘2’: 1275.8806303421597}, and in voltage: {‘2’: 0.06426138705935786} app DEBUG adc_reader
2024-06-10 14:50:07 Demo experiment pio1-worker1 2024-06-10T13:50:07.792216Z test_PD_is_near_0_volts_for_blank: :white_check_mark: app DEBUG self_test
2024-06-10 14:50:39 Demo experiment pio1-worker1 2024-06-10T13:50:39.409361Z Correlation between stirring RPM and duty cycle: 0.68 app DEBUG self_test
2024-06-10 14:50:39 Demo experiment pio1-worker1 2024-06-10T13:50:39.411519Z dcs=[36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], measured_rpms=[702.8769677677968, 954.7306247347872, 915.8362095986048, 860.7424363395329, 793.4205466894908, 718.8032575559811, 653.9033846572179, 570.3727931520718] app DEBUG self_test
2024-06-10 14:50:42 Demo experiment pio1-worker1 2024-06-10T13:50:42.657549Z RPM correlation not high enough: ([36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], [702.8769677677968, 954.7306247347872, 915.8362095986048, 860.7424363395329, 793.4205466894908, 718.8032575559811, 653.9033846572179, 570.3727931520718])
Traceback (most recent call last):
File /usr/local/lib/python3.11/dist-packages/pioreactor/actions/self_test.py, line 441, in _run
test(client, logger, unit, testing_experiment)
File /usr/local/lib/python3.11/dist-packages/pioreactor/actions/self_test.py, line 416, in test_positive_correlation_between_rpm_and_stirring
assert measured_correlation > 0.9, fRPM correlation not high enough: {(dcs, measured_rpms)}
^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: RPM correlation not high enough: ([36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], [702.8769677677968, 954.7306247347872, 915.8362095986048, 860.7424363395329, 793.4205466894908, 718.8032575559811, 653.9033846572179, 570.3727931520718])		 app DEBUG self_test
2024-06-10 14:50:42 Demo experiment pio1-worker1 2024-06-10T13:50:42.661618Z test positive correlation between rpm and stirring: RPM correlation not high enough: ([36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], [702.8769677677968, 954.7306247347872, 915.8362095986048, 860.7424363395329, 793.4205466894908, 718.8032575559811, 653.9033846572179, 570.3727931520718]) app WARNING self_test
2024-06-10 14:50:42 Demo experiment pio1-worker1 2024-06-10T13:50:42.663558Z test_positive_correlation_between_rpm_and_stirring: :x: app DEBUG self_test
2024-06-10 14:50:42 Demo experiment pio1-worker1 2024-06-10T13:50:42.666803Z 1 failed test :x: app INFO self_test
2024-06-10 14:55:48 Demo experiment pio1-worker1 2024-06-10T13:55:48.107326Z Init. app DEBUG stirring
2024-06-10 14:55:48 Demo experiment pio1-worker1 2024-06-10T13:55:48.186949Z Operating with RPM feedback loop. app DEBUG stirring
2024-06-10 14:55:48 Demo experiment pio1-worker1 2024-06-10T13:55:48.278833Z Initialized GPIO-17 using software-timing, initial frequency = 200.0 hz. app DEBUG PWM@GPIO-17
2024-06-10 14:55:48 Demo experiment pio1-worker1 2024-06-10T13:55:48.373837Z Ready. app INFO stirring
2024-06-10 14:55:48 Demo experiment pio1-worker1 2024-06-10T13:55:48.375826Z Starting stirring with 500.0 RPM. app DEBUG stirring
2024-06-10 14:55:48 Demo experiment pio1-worker1 2024-06-10T13:55:48.768811Z stirring is blocking until RPM is near 500.0. app DEBUG stirring
2024-06-10 14:56:07 Demo experiment pio1-worker1 2024-06-10T13:56:07.318395Z Cleaned up GPIO-17. app DEBUG PWM@GPIO-17
2024-06-10 14:56:07 Demo experiment pio1-worker1 2024-06-10T13:56:07.430329Z Waited 18.7 seconds for RPM to match, breaking out early. app DEBUG stirring
2024-06-10 14:56:07 Demo experiment pio1-worker1 2024-06-10T13:56:07.432263Z stirring is blocking until disconnected. app DEBUG stirring
2024-06-10 14:56:08 Demo experiment pio1-worker1 2024-06-10T13:56:08.381441Z Disconnected. app INFO stirring
2024-06-10 14:56:08 Demo experiment pio1-worker1 2024-06-10T13:56:08.384080Z Updated state from ready to disconnected. app INFO stirring
2024-06-10 14:56:08 Demo experiment pio1-worker1 2024-06-10T13:56:08.385782Z Exiting caused by Python atexit. app DEBUG stirring
2024-06-10 14:56:09 Demo experiment pio1-worker1 2024-06-10T13:56:09.389594Z Disconnected successfully from MQTT. app DEBUG stirring
2024-06-10 14:56:17 Demo experiment pio1-worker1 2024-06-10T13:56:17.455429Z Starting self-test. Running 10 tests. app INFO self_test
2024-06-10 14:56:17 Demo experiment pio1-worker1 2024-06-10T13:56:17.464429Z test_pioreactor_HAT_present: :white_check_mark: app DEBUG self_test
2024-06-10 14:56:17 Demo experiment pio1-worker1 2024-06-10T13:56:17.542331Z test_detect_heating_pcb: :white_check_mark: app DEBUG self_test
2024-06-10 14:56:17 Demo experiment pio1-worker1 2024-06-10T13:56:17.606892Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:56:17 Demo experiment pio1-worker1 2024-06-10T13:56:17.631601Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-10 14:56:18 Demo experiment pio1-worker1 2024-06-10T13:56:18.116703Z Varying heating. app DEBUG self_test
2024-06-10 14:56:33 Demo experiment pio1-worker1 2024-06-10T13:56:33.545210Z Correlation between temp sensor and heating: 0.96 app DEBUG self_test
2024-06-10 14:56:33 Demo experiment pio1-worker1 2024-06-10T13:56:33.781660Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:56:38 Demo experiment pio1-worker1 2024-06-10T13:56:38.617469Z test_positive_correlation_between_temperature_and_heating: :white_check_mark: app DEBUG self_test
2024-06-10 14:56:38 Demo experiment pio1-worker1 2024-06-10T13:56:38.622003Z test_aux_power_is_not_too_high: :white_check_mark: app DEBUG self_test
2024-06-10 14:57:05 Demo experiment pio1-worker1 2024-06-10T13:57:05.986067Z Corr(A, 1) = 1.0 app DEBUG self_test
2024-06-10 14:57:05 Demo experiment pio1-worker1 2024-06-10T13:57:05.988528Z [(32, 0.09879847628684894), (35, 0.1011295343044402), (53, 0.11742090077473251), (44, 0.10889710832460005), (38, 0.10327863100245081), (47, 0.11157189103351728), (50, 0.1140603670849366), (41, 0.10570228611981376), (56, 0.11896414511878191), (59, 0.12075645885129305), (62, 0.12298182042648491), (65, 0.12519441826942157)] app DEBUG self_test
2024-06-10 14:57:05 Demo experiment pio1-worker1 2024-06-10T13:57:05.990730Z Corr(A, 2) = 0.97 app DEBUG self_test
2024-06-10 14:57:05 Demo experiment pio1-worker1 2024-06-10T13:57:05.993064Z [(32, 0.0649137843111305), (35, 0.06498868326207896), (53, 0.06523821147376604), (44, 0.06506315778781292), (38, 0.06501655165752086), (47, 0.0651490587584162), (50, 0.06513120196905754), (41, 0.06500138626378936), (56, 0.06521344254751905), (59, 0.06522111022290128), (62, 0.06526235538721777), (65, 0.06530756420545264)] app DEBUG self_test
2024-06-10 14:57:09 Demo experiment pio1-worker1 2024-06-10T13:57:09.172025Z Correlations between LEDs and PD:
{(‘A’, ‘1’): 1.0, (‘A’, ‘2’): 0.97}		 app DEBUG self_test
2024-06-10 14:57:09 Demo experiment pio1-worker1 2024-06-10T13:57:09.175280Z test_all_positive_correlations_between_pds_and_leds: :white_check_mark: app DEBUG self_test
2024-06-10 14:57:09 Demo experiment pio1-worker1 2024-06-10T13:57:09.179591Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:57:09 Demo experiment pio1-worker1 2024-06-10T13:57:09.183238Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-10 14:57:10 Demo experiment pio1-worker1 2024-06-10T13:57:10.188183Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:57:10 Demo experiment pio1-worker1 2024-06-10T13:57:10.192620Z test_ambient_light_interference: :white_check_mark: app DEBUG self_test
2024-06-10 14:57:10 Demo experiment pio1-worker1 2024-06-10T13:57:10.196779Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:57:10 Demo experiment pio1-worker1 2024-06-10T13:57:10.199556Z ADC ready to read from PD channels 1, with gain 1. app DEBUG adc_reader
2024-06-10 14:57:11 Demo experiment pio1-worker1 2024-06-10T13:57:11.102928Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:57:11 Demo experiment pio1-worker1 2024-06-10T13:57:11.106307Z ADC offsets: {‘1’: 1269.9239904957828}, and in voltage: {‘1’: 0.06396137314768137} app DEBUG adc_reader
2024-06-10 14:57:18 Demo experiment pio1-worker1 2024-06-10T13:57:18.401048Z test_REF_is_lower_than_0_dot_256_volts: :white_check_mark: app DEBUG self_test
2024-06-10 14:57:19 Demo experiment pio1-worker1 2024-06-10T13:57:19.046674Z Not using any IR LED reference. app DEBUG ir_led_ref
2024-06-10 14:57:19 Demo experiment pio1-worker1 2024-06-10T13:57:19.072454Z Not using any calibration. app DEBUG calibration_transformer
2024-06-10 14:57:19 Demo experiment pio1-worker1 2024-06-10T13:57:19.404650Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:57:19 Demo experiment pio1-worker1 2024-06-10T13:57:19.408450Z ADC ready to read from PD channels 1, 2, with gain 1. app DEBUG adc_reader
2024-06-10 14:57:20 Demo experiment pio1-worker1 2024-06-10T13:57:20.447349Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:57:21 Demo experiment pio1-worker1 2024-06-10T13:57:21.353394Z ADC offsets: {‘1’: 1270.511340094112, ‘2’: 1276.6744958612148}, and in voltage: {‘1’: 0.06399095577397085, ‘2’: 0.06430137112854103} app DEBUG adc_reader
2024-06-10 14:58:33 Demo experiment pio1-worker1 2024-06-10T13:58:33.574878Z test_REF_is_in_correct_position: :white_check_mark: app DEBUG self_test
2024-06-10 14:58:33 Demo experiment pio1-worker1 2024-06-10T13:58:33.578296Z Not using any IR LED reference. app DEBUG ir_led_ref
2024-06-10 14:58:33 Demo experiment pio1-worker1 2024-06-10T13:58:33.580458Z Not using any calibration. app DEBUG calibration_transformer
2024-06-10 14:58:33 Demo experiment pio1-worker1 2024-06-10T13:58:33.883306Z Using ADC class Pico_ADC. app DEBUG adc_reader
2024-06-10 14:58:33 Demo experiment pio1-worker1 2024-06-10T13:58:33.886202Z ADC ready to read from PD channels 2, with gain 1. app DEBUG adc_reader
2024-06-10 14:58:34 Demo experiment pio1-worker1 2024-06-10T13:58:34.922158Z AC hz estimate: 50.0 app DEBUG adc_reader
2024-06-10 14:58:35 Demo experiment pio1-worker1 2024-06-10T13:58:35.825958Z ADC offsets: {‘2’: 1277.659469725304}, and in voltage: {‘2’: 0.06435098061803271} app DEBUG adc_reader
2024-06-10 14:58:49 Demo experiment pio1-worker1 2024-06-10T13:58:49.683532Z test_PD_is_near_0_volts_for_blank: :white_check_mark: app DEBUG self_test
2024-06-10 14:59:21 Demo experiment pio1-worker1 2024-06-10T13:59:21.214322Z Correlation between stirring RPM and duty cycle: -0.64 app DEBUG self_test
2024-06-10 14:59:21 Demo experiment pio1-worker1 2024-06-10T13:59:21.216538Z dcs=[36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], measured_rpms=[0.0, 0.0, 652.7621233556599, 806.364275115039, 755.2857653632436, 690.3322915398992, 620.9668134315133, 556.1104649286694] app DEBUG self_test
2024-06-10 14:59:24 Demo experiment pio1-worker1 2024-06-10T13:59:24.481567Z RPM correlation not high enough: ([36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], [0.0, 0.0, 652.7621233556599, 806.364275115039, 755.2857653632436, 690.3322915398992, 620.9668134315133, 556.1104649286694])
Traceback (most recent call last):
File /usr/local/lib/python3.11/dist-packages/pioreactor/actions/self_test.py, line 441, in _run
test(client, logger, unit, testing_experiment)
File /usr/local/lib/python3.11/dist-packages/pioreactor/actions/self_test.py, line 416, in test_positive_correlation_between_rpm_and_stirring
assert measured_correlation > 0.9, fRPM correlation not high enough: {(dcs, measured_rpms)}
^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: RPM correlation not high enough: ([36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], [0.0, 0.0, 652.7621233556599, 806.364275115039, 755.2857653632436, 690.3322915398992, 620.9668134315133, 556.1104649286694])		 app DEBUG self_test
2024-06-10 14:59:24 Demo experiment pio1-worker1 2024-06-10T13:59:24.485650Z test positive correlation between rpm and stirring: RPM correlation not high enough: ([36.0, 34.5, 33.0, 31.5, 30.0, 28.5, 27.0, 25.5], [0.0, 0.0, 652.7621233556599, 806.364275115039, 755.2857653632436, 690.3322915398992, 620.9668134315133, 556.1104649286694]) app WARNING self_test
2024-06-10 14:59:24 Demo experiment pio1-worker1 2024-06-10T13:59:24.487579Z test_positive_correlation_between_rpm_and_stirring: :x: app DEBUG self_test
2024-06-10 14:59:24 Demo experiment pio1-worker1 2024-06-10T13:59:24.490792Z 1 failed test :x: app INFO self_test
2024-06-10 15:09:26 Demo experiment pio1 2024-06-10T14:09:26.060154Z Starting export of tables: pioreactor_unit_activity_data, logs. app INFO export_experiment_data
4

Hi @TimSkvortsov,

I think this is okay. It looks like the fan might be spinning too fast for the RPM sensor to detect it at high voltages. Optional: I suggest slightly reducing the configuration option [stirring] initial_duty_cycle from 30 to 25.

5

Thanks @CamDavidsonPilon. The fan starts spinning on its own about half of the time when I control it manually (Manage → Stirring ON), but does not start spinning in the self-test(or stops spinning mid-test) until given a light nudge with a pencil. I have tried varying the initial_duty_cycle parameter between 20 and 40 and also adjusting the distance between the fan and the vial holder, but without much success.

6

So the fan will start and stop frequently during the self-test (about half the tests utilize the fan for various functions).

However, the larger issue is that the fan often doesn’t start when you command it from the (Manage → Stirring ON) workflow. Some steps:

  1. Increase the initial_duty_cycle to a high value, like 40 or 50, or higher.
  2. See if you can increase the distance more.

If this ^ doesn’t work, we may have to send you up-rev version of the top-faceplate that increases this gap by 0.2mm. Send me an email at cam@pioreactor.com.